pett at cgl.ucsf.edu
Tue May 3 15:15:56 PDT 2005
On May 2, 2005, at 7:25 PM, Bryan W. Lepore wrote:
> hi Eric
> On Mon, 2 May 2005, Eric Pettersen wrote:
>> mmaker is a command for use in Chimera's "internal" command
>> It can be included inside scripts that are run from the Unix command
>> line though.
> so like this?:
> chimera --nogui << eof
> this fails, but there's no output, hence the email.
Chimera can handle two kinds of script files: those containing Chimera
command-line commands (file name ending in .com or .cmd or preceded
with cmd: or com: on the Unix Chimera startup command-line) and Python
files (.py ending or py: prefix).
So if you had a file named "domatch" that contained:
mmaker #0 #1 pair bb
write #1 transformed.pdb
and executed chimera as "chimera --nogui cmd:domatch" then file2 would
be superimposed on file1 and the transformed coordinates of file2 would
be written out to transformed.pdb
>> If you briefly outlined what you want to do, I could provide better
>> advice about your best approach.
> take a list of .ent files and generate a superposition-based sequence
> alignment. i can do this ok with the gui.
There are no Chimera commands that write sequence alignments, so this
can only be done using Chimera's Python layer.
I've appended a Python script that does the following:
1) reads a file named "structList" that has lines consisting of 3 file
names: 2 PDB files and an output alignment file
2) uses MatchMaker to superimpose the structures
3) uses the "iterate match" capability of Multalign Viewer to improve
the superposition by pruning off long residue pairings and rematching
4) creates a superposition-based sequence alignment using Match->Align
5) uses Multalign Viewer again to write out the alignment
Now, the script can't be run in nogui mode since Multalign Viewer is
gui-only at this point. Nonetheless, it does run without user
intervention, so you can just leave it running on a display you aren't
using. There are comments in the script about what the code is doing
and what various options are. Let me know if you have questions.
I should also note that the script is using Needleman-Wunsch to do the
initial sequence alignment. If your structures have low sequence
identity, you might want to switch to Smith-Waterman instead. I am
working on an improvement for MatchMaker that will make it much better
at matching low sequence identity structures (it will consider
secondary structure in addition to residue type). I could send you the
new version when it's ready in a few days if the current MatchMaker has
trouble on your data.
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